3AA2

A52I E. coli RNase HI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI

Tanaka, M.Chon, H.Angkawidjaja, C.Koga, Y.Takano, K.Kanaya, S.

(2010) Protein Pept Lett 17: 1163-1169

  • DOI: https://doi.org/10.2174/092986610791760342
  • Primary Citation of Related Structures:  
    3AA2, 3AA3, 3AA4, 3AA5

  • PubMed Abstract: 

    It has generally been accepted that an increase in protein stability is proportional to the increase in hydrophobicity. When a cavity is created by large-to-small substitutions of amino acid residues in protein cores, protein stability decreases 5.3 kJ/mol per single methyl(ene) group removal. In contrast, many reported cavity-filling mutations either failed to increase stability or produced marginal increases in stability; even in successful cases, the increase in stability was much lower than expected from the cost of single methyl(ene) group removal in cavity-creating mutations. Previously it was found that some cavity-filling mutant proteins at Ala52 in E. coli RNase HI increased stability, but decreased activity and they did not increase the stability to the degree expected by the hydrophobic effect alone. The present study attempted to structurally analyze these variant proteins, and it was found that substitutions have little effect on the overall fold but cause conformational strains with the neighboring residues. The present results and literature on cavity-creating/-filling variants provide insight into protein architecture, indicating that natural protein cores are able to accommodate larger side-chain residue by substitution; in other words, excess-packing may not be chosen in natural selection.


  • Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease HI155Escherichia coli K-12Mutation(s): 1 
EC: 3.1.26.4
UniProt
Find proteins for P0A7Y4 (Escherichia coli (strain K12))
Explore P0A7Y4 
Go to UniProtKB:  P0A7Y4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Y4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.368α = 90
b = 85.301β = 90
c = 36.253γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2010-10-06 
  • Deposition Author(s): Takano, K.

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references